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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.8

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-02-21, 11:00 based on data in: /data1/meaneylab/pbordi/rna_seq/MIA


        General Statistics

        Showing 292/292 rows and 9/11 columns.
        Sample Name% Dups% AlignedM Aligned% AlignedM Aligned% Trimmed% Dups% GCM Seqs
        D8.06_38_dHIP
        0.2%
        0.1
        G9.03_32_ACC
        0.3%
        0.1
        NS.1223.004.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.03_32_vHIP
        20.7%
        94.3%
        44.7
        NS.1223.004.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.03_32_vHIP_R1
        56.8%
        51%
        47.4
        NS.1223.004.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.03_32_vHIP_R2
        1.7%
        60.2%
        52%
        47.4
        NS.1223.004.NEBNext_dual_i7_A1---NEBNext_dual_i5_A1.03_32_vHIPest_lib_complex_metrics
        18.8%
        NS.1223.004.NEBNext_dual_i7_A2---NEBNext_dual_i5_A2.17_32_dHIP
        24.3%
        94.6%
        49.7
        NS.1223.004.NEBNext_dual_i7_A2---NEBNext_dual_i5_A2.17_32_dHIP_R1
        57.8%
        52%
        52.5
        NS.1223.004.NEBNext_dual_i7_A2---NEBNext_dual_i5_A2.17_32_dHIP_R2
        1.7%
        60.8%
        52%
        52.5
        NS.1223.004.NEBNext_dual_i7_A2---NEBNext_dual_i5_A2.17_32_dHIPest_lib_complex_metrics
        22.2%
        NS.1223.004.NEBNext_dual_i7_A3---NEBNext_dual_i5_A3.07_26_ACC
        20.5%
        94.0%
        45.3
        NS.1223.004.NEBNext_dual_i7_A3---NEBNext_dual_i5_A3.07_26_ACC_R1
        56.9%
        51%
        48.1
        NS.1223.004.NEBNext_dual_i7_A3---NEBNext_dual_i5_A3.07_26_ACC_R2
        1.7%
        60.7%
        52%
        48.1
        NS.1223.004.NEBNext_dual_i7_A3---NEBNext_dual_i5_A3.07_26_ACCest_lib_complex_metrics
        18.6%
        NS.1223.004.NEBNext_dual_i7_A4---NEBNext_dual_i5_A4.10_35_vHIP
        20.7%
        94.2%
        44.3
        NS.1223.004.NEBNext_dual_i7_A4---NEBNext_dual_i5_A4.10_35_vHIP_R1
        55.9%
        51%
        47.0
        NS.1223.004.NEBNext_dual_i7_A4---NEBNext_dual_i5_A4.10_35_vHIP_R2
        1.8%
        58.8%
        51%
        47.0
        NS.1223.004.NEBNext_dual_i7_A4---NEBNext_dual_i5_A4.10_35_vHIPest_lib_complex_metrics
        18.7%
        NS.1223.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.08_31_dHIP
        19.9%
        94.3%
        42.0
        NS.1223.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.08_31_dHIP_R1
        56.0%
        51%
        44.5
        NS.1223.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.08_31_dHIP_R2
        1.8%
        58.2%
        51%
        44.5
        NS.1223.004.NEBNext_dual_i7_A5---NEBNext_dual_i5_A5.08_31_dHIPest_lib_complex_metrics
        18.0%
        NS.1223.004.NEBNext_dual_i7_A6---NEBNext_dual_i5_A6.24_32_ACC
        19.8%
        93.7%
        60.0
        NS.1223.004.NEBNext_dual_i7_A6---NEBNext_dual_i5_A6.24_32_ACC_R1
        57.7%
        50%
        64.0
        NS.1223.004.NEBNext_dual_i7_A6---NEBNext_dual_i5_A6.24_32_ACC_R2
        1.8%
        61.1%
        50%
        64.0
        NS.1223.004.NEBNext_dual_i7_A6---NEBNext_dual_i5_A6.24_32_ACCest_lib_complex_metrics
        17.8%
        NS.1223.004.NEBNext_dual_i7_A7---NEBNext_dual_i5_A7.01_15_vHIP
        19.9%
        94.3%
        53.6
        NS.1223.004.NEBNext_dual_i7_A7---NEBNext_dual_i5_A7.01_15_vHIP_R1
        57.7%
        51%
        56.8
        NS.1223.004.NEBNext_dual_i7_A7---NEBNext_dual_i5_A7.01_15_vHIP_R2
        1.7%
        60.6%
        51%
        56.8
        NS.1223.004.NEBNext_dual_i7_A7---NEBNext_dual_i5_A7.01_15_vHIPest_lib_complex_metrics
        18.0%
        NS.1223.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.05_13_dHIP
        20.3%
        94.4%
        62.8
        NS.1223.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.05_13_dHIP_R1
        58.6%
        51%
        66.5
        NS.1223.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.05_13_dHIP_R2
        1.6%
        61.5%
        51%
        66.5
        NS.1223.004.NEBNext_dual_i7_A8---NEBNext_dual_i5_A8.05_13_dHIPest_lib_complex_metrics
        18.3%
        NS.1223.004.NEBNext_dual_i7_A9---NEBNext_dual_i5_A9.01_09_ACC
        22.0%
        93.7%
        52.0
        NS.1223.004.NEBNext_dual_i7_A9---NEBNext_dual_i5_A9.01_09_ACC_R1
        57.0%
        51%
        55.6
        NS.1223.004.NEBNext_dual_i7_A9---NEBNext_dual_i5_A9.01_09_ACC_R2
        1.9%
        60.0%
        51%
        55.6
        NS.1223.004.NEBNext_dual_i7_A9---NEBNext_dual_i5_A9.01_09_ACCest_lib_complex_metrics
        19.9%
        NS.1223.004.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.16_38_ACC
        20.9%
        93.7%
        33.3
        NS.1223.004.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.16_38_ACC_R1
        53.6%
        51%
        35.5
        NS.1223.004.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.16_38_ACC_R2
        1.8%
        56.2%
        51%
        35.5
        NS.1223.004.NEBNext_dual_i7_B1---NEBNext_dual_i5_B1.16_38_ACCest_lib_complex_metrics
        19.0%
        NS.1223.004.NEBNext_dual_i7_B2---NEBNext_dual_i5_B2.17_32_vHIP
        21.2%
        94.1%
        50.0
        NS.1223.004.NEBNext_dual_i7_B2---NEBNext_dual_i5_B2.17_32_vHIP_R1
        57.9%
        51%
        53.1
        NS.1223.004.NEBNext_dual_i7_B2---NEBNext_dual_i5_B2.17_32_vHIP_R2
        1.8%
        61.3%
        51%
        53.1
        NS.1223.004.NEBNext_dual_i7_B2---NEBNext_dual_i5_B2.17_32_vHIPest_lib_complex_metrics
        19.1%
        NS.1223.004.NEBNext_dual_i7_B3---NEBNext_dual_i5_B3.07_26_dHIP
        22.0%
        94.4%
        51.1
        NS.1223.004.NEBNext_dual_i7_B3---NEBNext_dual_i5_B3.07_26_dHIP_R1
        58.7%
        51%
        54.1
        NS.1223.004.NEBNext_dual_i7_B3---NEBNext_dual_i5_B3.07_26_dHIP_R2
        1.8%
        61.7%
        52%
        54.1
        NS.1223.004.NEBNext_dual_i7_B3---NEBNext_dual_i5_B3.07_26_dHIPest_lib_complex_metrics
        19.8%
        NS.1223.004.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.23_38_ACC
        19.4%
        93.9%
        36.9
        NS.1223.004.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.23_38_ACC_R1
        54.0%
        51%
        39.3
        NS.1223.004.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.23_38_ACC_R2
        1.7%
        56.9%
        51%
        39.3
        NS.1223.004.NEBNext_dual_i7_B4---NEBNext_dual_i5_B4.23_38_ACCest_lib_complex_metrics
        17.7%
        NS.1223.004.NEBNext_dual_i7_B5---NEBNext_dual_i5_B5.08_31_vHIP
        18.4%
        94.4%
        33.7
        NS.1223.004.NEBNext_dual_i7_B5---NEBNext_dual_i5_B5.08_31_vHIP_R1
        54.8%
        51%
        35.7
        NS.1223.004.NEBNext_dual_i7_B5---NEBNext_dual_i5_B5.08_31_vHIP_R2
        1.7%
        57.8%
        52%
        35.7
        NS.1223.004.NEBNext_dual_i7_B5---NEBNext_dual_i5_B5.08_31_vHIPest_lib_complex_metrics
        16.7%
        NS.1223.004.NEBNext_dual_i7_B6---NEBNext_dual_i5_B6.24_32_dHIP
        21.5%
        94.2%
        39.5
        NS.1223.004.NEBNext_dual_i7_B6---NEBNext_dual_i5_B6.24_32_dHIP_R1
        54.3%
        51%
        41.9
        NS.1223.004.NEBNext_dual_i7_B6---NEBNext_dual_i5_B6.24_32_dHIP_R2
        1.8%
        56.8%
        51%
        41.9
        NS.1223.004.NEBNext_dual_i7_B6---NEBNext_dual_i5_B6.24_32_dHIPest_lib_complex_metrics
        19.7%
        NS.1223.004.NEBNext_dual_i7_B7---NEBNext_dual_i5_B7.07_09_ACC
        19.4%
        94.0%
        42.9
        NS.1223.004.NEBNext_dual_i7_B7---NEBNext_dual_i5_B7.07_09_ACC_R1
        54.4%
        51%
        45.6
        NS.1223.004.NEBNext_dual_i7_B7---NEBNext_dual_i5_B7.07_09_ACC_R2
        1.8%
        57.8%
        51%
        45.6
        NS.1223.004.NEBNext_dual_i7_B7---NEBNext_dual_i5_B7.07_09_ACCest_lib_complex_metrics
        17.6%
        NS.1223.004.NEBNext_dual_i7_B8---NEBNext_dual_i5_B8.05_13_vHIP
        21.3%
        94.2%
        56.0
        NS.1223.004.NEBNext_dual_i7_B8---NEBNext_dual_i5_B8.05_13_vHIP_R1
        57.9%
        51%
        59.4
        NS.1223.004.NEBNext_dual_i7_B8---NEBNext_dual_i5_B8.05_13_vHIP_R2
        1.8%
        60.5%
        52%
        59.4
        NS.1223.004.NEBNext_dual_i7_B8---NEBNext_dual_i5_B8.05_13_vHIPest_lib_complex_metrics
        19.2%
        NS.1223.004.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.01_09_dHIP
        21.5%
        94.4%
        49.6
        NS.1223.004.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.01_09_dHIP_R1
        57.4%
        51%
        52.6
        NS.1223.004.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.01_09_dHIP_R2
        1.8%
        60.0%
        52%
        52.6
        NS.1223.004.NEBNext_dual_i7_B9---NEBNext_dual_i5_B9.01_09_dHIPest_lib_complex_metrics
        19.5%
        NS.1223.004.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.16_38_dHIP
        18.6%
        94.3%
        32.8
        NS.1223.004.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.16_38_dHIP_R1
        50.9%
        51%
        34.7
        NS.1223.004.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.16_38_dHIP_R2
        1.8%
        53.1%
        51%
        34.7
        NS.1223.004.NEBNext_dual_i7_C1---NEBNext_dual_i5_C1.16_38_dHIPest_lib_complex_metrics
        17.0%
        NS.1223.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.03_13_ACC
        18.5%
        93.8%
        28.0
        NS.1223.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.03_13_ACC_R1
        50.4%
        50%
        29.9
        NS.1223.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.03_13_ACC_R2
        1.7%
        53.6%
        51%
        29.9
        NS.1223.004.NEBNext_dual_i7_C2---NEBNext_dual_i5_C2.03_13_ACCest_lib_complex_metrics
        16.9%
        NS.1223.004.NEBNext_dual_i7_C3---NEBNext_dual_i5_C3.07_26_vHIP
        21.2%
        94.3%
        44.5
        NS.1223.004.NEBNext_dual_i7_C3---NEBNext_dual_i5_C3.07_26_vHIP_R1
        57.1%
        51%
        47.2
        NS.1223.004.NEBNext_dual_i7_C3---NEBNext_dual_i5_C3.07_26_vHIP_R2
        1.7%
        61.1%
        52%
        47.2
        NS.1223.004.NEBNext_dual_i7_C3---NEBNext_dual_i5_C3.07_26_vHIPest_lib_complex_metrics
        19.2%
        NS.1223.004.NEBNext_dual_i7_C4---NEBNext_dual_i5_C4.23_38_dHIP
        17.5%
        94.5%
        28.6
        NS.1223.004.NEBNext_dual_i7_C4---NEBNext_dual_i5_C4.23_38_dHIP_R1
        49.0%
        51%
        30.3
        NS.1223.004.NEBNext_dual_i7_C4---NEBNext_dual_i5_C4.23_38_dHIP_R2
        1.7%
        52.2%
        51%
        30.3
        NS.1223.004.NEBNext_dual_i7_C4---NEBNext_dual_i5_C4.23_38_dHIPest_lib_complex_metrics
        16.0%
        NS.1223.004.NEBNext_dual_i7_C5---NEBNext_dual_i5_C5.19_26_ACC
        21.8%
        93.7%
        34.0
        NS.1223.004.NEBNext_dual_i7_C5---NEBNext_dual_i5_C5.19_26_ACC_R1
        54.4%
        51%
        36.3
        NS.1223.004.NEBNext_dual_i7_C5---NEBNext_dual_i5_C5.19_26_ACC_R2
        1.8%
        57.3%
        51%
        36.3
        NS.1223.004.NEBNext_dual_i7_C5---NEBNext_dual_i5_C5.19_26_ACCest_lib_complex_metrics
        20.0%
        NS.1223.004.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.24_32_vHIP
        19.1%
        94.2%
        26.7
        NS.1223.004.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.24_32_vHIP_R1
        51.7%
        52%
        28.4
        NS.1223.004.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.24_32_vHIP_R2
        1.7%
        54.7%
        52%
        28.4
        NS.1223.004.NEBNext_dual_i7_C6---NEBNext_dual_i5_C6.24_32_vHIPest_lib_complex_metrics
        17.4%
        NS.1223.004.NEBNext_dual_i7_C7---NEBNext_dual_i5_C7.07_09_dHIP
        23.7%
        94.3%
        43.0
        NS.1223.004.NEBNext_dual_i7_C7---NEBNext_dual_i5_C7.07_09_dHIP_R1
        55.9%
        51%
        45.6
        NS.1223.004.NEBNext_dual_i7_C7---NEBNext_dual_i5_C7.07_09_dHIP_R2
        1.6%
        59.1%
        51%
        45.6
        NS.1223.004.NEBNext_dual_i7_C7---NEBNext_dual_i5_C7.07_09_dHIPest_lib_complex_metrics
        21.9%
        NS.1223.004.NEBNext_dual_i7_C8---NEBNext_dual_i5_C8.06_38_ACC
        18.4%
        94.1%
        28.0
        NS.1223.004.NEBNext_dual_i7_C8---NEBNext_dual_i5_C8.06_38_ACC_R1
        51.2%
        51%
        29.7
        NS.1223.004.NEBNext_dual_i7_C8---NEBNext_dual_i5_C8.06_38_ACC_R2
        1.7%
        53.7%
        52%
        29.7
        NS.1223.004.NEBNext_dual_i7_C8---NEBNext_dual_i5_C8.06_38_ACCest_lib_complex_metrics
        16.8%
        NS.1223.004.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.01_09_vHIP
        18.2%
        94.4%
        27.6
        NS.1223.004.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.01_09_vHIP_R1
        51.2%
        52%
        29.2
        NS.1223.004.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.01_09_vHIP_R2
        1.8%
        54.2%
        52%
        29.2
        NS.1223.004.NEBNext_dual_i7_C9---NEBNext_dual_i5_C9.01_09_vHIPest_lib_complex_metrics
        16.6%
        NS.1223.004.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.16_38_vHIP
        19.5%
        94.5%
        32.6
        NS.1223.004.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.16_38_vHIP_R1
        52.3%
        51%
        34.4
        NS.1223.004.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.16_38_vHIP_R2
        1.8%
        55.2%
        51%
        34.4
        NS.1223.004.NEBNext_dual_i7_D1---NEBNext_dual_i5_D1.16_38_vHIPest_lib_complex_metrics
        17.9%
        NS.1223.004.NEBNext_dual_i7_D2---NEBNext_dual_i5_D2.03_13_dHIP
        21.7%
        94.5%
        51.0
        NS.1223.004.NEBNext_dual_i7_D2---NEBNext_dual_i5_D2.03_13_dHIP_R1
        56.6%
        51%
        54.0
        NS.1223.004.NEBNext_dual_i7_D2---NEBNext_dual_i5_D2.03_13_dHIP_R2
        1.7%
        60.0%
        51%
        54.0
        NS.1223.004.NEBNext_dual_i7_D2---NEBNext_dual_i5_D2.03_13_dHIPest_lib_complex_metrics
        19.8%
        NS.1223.004.NEBNext_dual_i7_D3---NEBNext_dual_i5_D3.14_35_ACC
        19.2%
        93.9%
        30.0
        NS.1223.004.NEBNext_dual_i7_D3---NEBNext_dual_i5_D3.14_35_ACC_R1
        51.6%
        51%
        31.9
        NS.1223.004.NEBNext_dual_i7_D3---NEBNext_dual_i5_D3.14_35_ACC_R2
        1.8%
        54.6%
        51%
        31.9
        NS.1223.004.NEBNext_dual_i7_D3---NEBNext_dual_i5_D3.14_35_ACCest_lib_complex_metrics
        17.5%
        NS.1223.004.NEBNext_dual_i7_D4---NEBNext_dual_i5_D4.23_38_vHIP
        18.0%
        94.2%
        25.4
        NS.1223.004.NEBNext_dual_i7_D4---NEBNext_dual_i5_D4.23_38_vHIP_R1
        51.2%
        51%
        26.9
        NS.1223.004.NEBNext_dual_i7_D4---NEBNext_dual_i5_D4.23_38_vHIP_R2
        1.7%
        54.7%
        51%
        26.9
        NS.1223.004.NEBNext_dual_i7_D4---NEBNext_dual_i5_D4.23_38_vHIPest_lib_complex_metrics
        16.4%
        NS.1223.004.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.19_26_dHIP
        18.9%
        94.2%
        24.4
        NS.1223.004.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.19_26_dHIP_R1
        49.5%
        51%
        25.9
        NS.1223.004.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.19_26_dHIP_R2
        2.0%
        51.3%
        51%
        25.9
        NS.1223.004.NEBNext_dual_i7_D5---NEBNext_dual_i5_D5.19_26_dHIPest_lib_complex_metrics
        17.4%
        NS.1223.004.NEBNext_dual_i7_D6---NEBNext_dual_i5_D6.21_38_ACC
        18.7%
        94.1%
        40.8
        NS.1223.004.NEBNext_dual_i7_D6---NEBNext_dual_i5_D6.21_38_ACC_R1
        54.8%
        51%
        43.3
        NS.1223.004.NEBNext_dual_i7_D6---NEBNext_dual_i5_D6.21_38_ACC_R2
        1.7%
        57.5%
        51%
        43.3
        NS.1223.004.NEBNext_dual_i7_D6---NEBNext_dual_i5_D6.21_38_ACCest_lib_complex_metrics
        16.9%
        NS.1223.004.NEBNext_dual_i7_D7---NEBNext_dual_i5_D7.07_09_vHIP
        17.4%
        94.3%
        27.2
        NS.1223.004.NEBNext_dual_i7_D7---NEBNext_dual_i5_D7.07_09_vHIP_R1
        50.0%
        51%
        28.9
        NS.1223.004.NEBNext_dual_i7_D7---NEBNext_dual_i5_D7.07_09_vHIP_R2
        1.8%
        53.5%
        52%
        28.9
        NS.1223.004.NEBNext_dual_i7_D7---NEBNext_dual_i5_D7.07_09_vHIPest_lib_complex_metrics
        15.8%
        NS.1223.004.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.06_38_dHIP
        20.8%
        94.6%
        36.1
        NS.1223.004.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.06_38_dHIP_R1
        54.6%
        51%
        38.2
        NS.1223.004.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.06_38_dHIP_R2
        1.7%
        57.9%
        52%
        38.2
        NS.1223.004.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.06_38_dHIP_est_lib_complex_metrics
        19.1%
        NS.1223.004.NEBNext_dual_i7_D8---NEBNext_dual_i5_D8.06_38_dHIPest_lib_complex_metrics
        19.1%
        NS.1223.004.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.03_15_ACC
        17.0%
        93.9%
        24.1
        NS.1223.004.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.03_15_ACC_R1
        48.4%
        51%
        25.7
        NS.1223.004.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.03_15_ACC_R2
        1.8%
        51.6%
        52%
        25.7
        NS.1223.004.NEBNext_dual_i7_D9---NEBNext_dual_i5_D9.03_15_ACCest_lib_complex_metrics
        15.5%
        NS.1223.004.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.27_32_ACC
        18.7%
        94.0%
        27.5
        NS.1223.004.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.27_32_ACC_R1
        49.6%
        51%
        29.2
        NS.1223.004.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.27_32_ACC_R2
        1.7%
        52.9%
        52%
        29.2
        NS.1223.004.NEBNext_dual_i7_E1---NEBNext_dual_i5_E1.27_32_ACCest_lib_complex_metrics
        17.2%
        NS.1223.004.NEBNext_dual_i7_E2---NEBNext_dual_i5_E2.03_13_vHIP
        19.3%
        94.2%
        34.9
        NS.1223.004.NEBNext_dual_i7_E2---NEBNext_dual_i5_E2.03_13_vHIP_R1
        53.2%
        51%
        37.0
        NS.1223.004.NEBNext_dual_i7_E2---NEBNext_dual_i5_E2.03_13_vHIP_R2
        1.8%
        55.3%
        51%
        37.0
        NS.1223.004.NEBNext_dual_i7_E2---NEBNext_dual_i5_E2.03_13_vHIPest_lib_complex_metrics
        17.6%
        NS.1223.004.NEBNext_dual_i7_E3---NEBNext_dual_i5_E3.14_35_dHIP
        19.6%
        94.4%
        54.3
        NS.1223.004.NEBNext_dual_i7_E3---NEBNext_dual_i5_E3.14_35_dHIP_R1
        56.9%
        51%
        57.5
        NS.1223.004.NEBNext_dual_i7_E3---NEBNext_dual_i5_E3.14_35_dHIP_R2
        1.7%
        60.7%
        51%
        57.5
        NS.1223.004.NEBNext_dual_i7_E3---NEBNext_dual_i5_E3.14_35_dHIPest_lib_complex_metrics
        17.7%
        NS.1223.004.NEBNext_dual_i7_E4---NEBNext_dual_i5_E4.04_09_ACC
        20.1%
        94.0%
        33.1
        NS.1223.004.NEBNext_dual_i7_E4---NEBNext_dual_i5_E4.04_09_ACC_R1
        53.5%
        51%
        35.2
        NS.1223.004.NEBNext_dual_i7_E4---NEBNext_dual_i5_E4.04_09_ACC_R2
        1.7%
        56.7%
        52%
        35.2
        NS.1223.004.NEBNext_dual_i7_E4---NEBNext_dual_i5_E4.04_09_ACCest_lib_complex_metrics
        18.4%
        NS.1223.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.19_26_vHIP
        20.3%
        94.1%
        32.9
        NS.1223.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.19_26_vHIP_R1
        54.5%
        51%
        35.0
        NS.1223.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.19_26_vHIP_R2
        1.8%
        57.7%
        51%
        35.0
        NS.1223.004.NEBNext_dual_i7_E5---NEBNext_dual_i5_E5.19_26_vHIPest_lib_complex_metrics
        18.5%
        NS.1223.004.NEBNext_dual_i7_E6---NEBNext_dual_i5_E6.21_38_dHIP
        17.5%
        94.5%
        27.6
        NS.1223.004.NEBNext_dual_i7_E6---NEBNext_dual_i5_E6.21_38_dHIP_R1
        50.7%
        51%
        29.2
        NS.1223.004.NEBNext_dual_i7_E6---NEBNext_dual_i5_E6.21_38_dHIP_R2
        1.9%
        52.6%
        52%
        29.2
        NS.1223.004.NEBNext_dual_i7_E6---NEBNext_dual_i5_E6.21_38_dHIPest_lib_complex_metrics
        16.0%
        NS.1223.004.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.25_31_ACC
        16.7%
        94.2%
        24.1
        NS.1223.004.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.25_31_ACC_R1
        49.0%
        51%
        25.6
        NS.1223.004.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.25_31_ACC_R2
        1.5%
        52.3%
        51%
        25.6
        NS.1223.004.NEBNext_dual_i7_E7---NEBNext_dual_i5_E7.25_31_ACCest_lib_complex_metrics
        15.4%
        NS.1223.004.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.06_38_vHIP
        20.2%
        94.3%
        38.5
        NS.1223.004.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.06_38_vHIP_R1
        55.3%
        51%
        40.8
        NS.1223.004.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.06_38_vHIP_R2
        1.7%
        58.8%
        52%
        40.8
        NS.1223.004.NEBNext_dual_i7_E8---NEBNext_dual_i5_E8.06_38_vHIPest_lib_complex_metrics
        18.3%
        NS.1223.004.NEBNext_dual_i7_E9---NEBNext_dual_i5_E9.03_15_dHIP
        16.4%
        94.5%
        27.6
        NS.1223.004.NEBNext_dual_i7_E9---NEBNext_dual_i5_E9.03_15_dHIP_R1
        48.2%
        51%
        29.2
        NS.1223.004.NEBNext_dual_i7_E9---NEBNext_dual_i5_E9.03_15_dHIP_R2
        1.9%
        51.1%
        51%
        29.2
        NS.1223.004.NEBNext_dual_i7_E9---NEBNext_dual_i5_E9.03_15_dHIPest_lib_complex_metrics
        15.0%
        NS.1223.004.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.27_32_dHIP
        18.2%
        94.5%
        26.0
        NS.1223.004.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.27_32_dHIP_R1
        49.3%
        51%
        27.6
        NS.1223.004.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.27_32_dHIP_R2
        1.7%
        52.7%
        51%
        27.6
        NS.1223.004.NEBNext_dual_i7_F1---NEBNext_dual_i5_F1.27_32_dHIPest_lib_complex_metrics
        16.7%
        NS.1223.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.08_09_ACC
        18.5%
        93.9%
        32.9
        NS.1223.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.08_09_ACC_R1
        52.1%
        51%
        35.1
        NS.1223.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.08_09_ACC_R2
        1.8%
        55.1%
        51%
        35.1
        NS.1223.004.NEBNext_dual_i7_F2---NEBNext_dual_i5_F2.08_09_ACCest_lib_complex_metrics
        16.8%
        NS.1223.004.NEBNext_dual_i7_F3---NEBNext_dual_i5_F3.14_35_vHIP
        17.2%
        94.2%
        23.6
        NS.1223.004.NEBNext_dual_i7_F3---NEBNext_dual_i5_F3.14_35_vHIP_R1
        50.0%
        51%
        25.1
        NS.1223.004.NEBNext_dual_i7_F3---NEBNext_dual_i5_F3.14_35_vHIP_R2
        1.8%
        52.8%
        51%
        25.1
        NS.1223.004.NEBNext_dual_i7_F3---NEBNext_dual_i5_F3.14_35_vHIPest_lib_complex_metrics
        15.7%
        NS.1223.004.NEBNext_dual_i7_F4---NEBNext_dual_i5_F4.04_09_dHIP
        15.4%
        94.2%
        20.1
        NS.1223.004.NEBNext_dual_i7_F4---NEBNext_dual_i5_F4.04_09_dHIP_R1
        46.1%
        51%
        21.3
        NS.1223.004.NEBNext_dual_i7_F4---NEBNext_dual_i5_F4.04_09_dHIP_R2
        1.8%
        48.8%
        51%
        21.3
        NS.1223.004.NEBNext_dual_i7_F4---NEBNext_dual_i5_F4.04_09_dHIPest_lib_complex_metrics
        14.1%
        NS.1223.004.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.13_09_ACC
        18.9%
        93.8%
        31.8
        NS.1223.004.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.13_09_ACC_R1
        51.1%
        50%
        33.9
        NS.1223.004.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.13_09_ACC_R2
        1.9%
        53.9%
        51%
        33.9
        NS.1223.004.NEBNext_dual_i7_F5---NEBNext_dual_i5_F5.13_09_ACCest_lib_complex_metrics
        17.4%
        NS.1223.004.NEBNext_dual_i7_F6---NEBNext_dual_i5_F6.21_38_vHIP
        20.6%
        94.2%
        31.9
        NS.1223.004.NEBNext_dual_i7_F6---NEBNext_dual_i5_F6.21_38_vHIP_R1
        52.7%
        52%
        33.8
        NS.1223.004.NEBNext_dual_i7_F6---NEBNext_dual_i5_F6.21_38_vHIP_R2
        1.8%
        55.3%
        52%
        33.8
        NS.1223.004.NEBNext_dual_i7_F6---NEBNext_dual_i5_F6.21_38_vHIPest_lib_complex_metrics
        18.9%
        NS.1223.004.NEBNext_dual_i7_F7---NEBNext_dual_i5_F7.25_31_dHIP
        19.1%
        94.5%
        33.2
        NS.1223.004.NEBNext_dual_i7_F7---NEBNext_dual_i5_F7.25_31_dHIP_R1
        52.8%
        51%
        35.1
        NS.1223.004.NEBNext_dual_i7_F7---NEBNext_dual_i5_F7.25_31_dHIP_R2
        1.7%
        56.5%
        51%
        35.1
        NS.1223.004.NEBNext_dual_i7_F7---NEBNext_dual_i5_F7.25_31_dHIPest_lib_complex_metrics
        17.5%
        NS.1223.004.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.11_09_ACC
        17.5%
        93.5%
        24.1
        NS.1223.004.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.11_09_ACC_R1
        49.5%
        51%
        25.8
        NS.1223.004.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.11_09_ACC_R2
        1.7%
        52.5%
        51%
        25.8
        NS.1223.004.NEBNext_dual_i7_F8---NEBNext_dual_i5_F8.11_09_ACCest_lib_complex_metrics
        16.0%
        NS.1223.004.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.03_15_vHIP
        24.6%
        94.3%
        64.7
        NS.1223.004.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.03_15_vHIP_R1
        61.1%
        51%
        68.6
        NS.1223.004.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.03_15_vHIP_R2
        1.7%
        64.3%
        52%
        68.6
        NS.1223.004.NEBNext_dual_i7_F9---NEBNext_dual_i5_F9.03_15_vHIPest_lib_complex_metrics
        22.3%
        NS.1223.004.NEBNext_dual_i7_G1---NEBNext_dual_i5_G1.27_32_vHIP
        18.3%
        94.2%
        27.4
        NS.1223.004.NEBNext_dual_i7_G1---NEBNext_dual_i5_G1.27_32_vHIP_R1
        52.2%
        51%
        29.1
        NS.1223.004.NEBNext_dual_i7_G1---NEBNext_dual_i5_G1.27_32_vHIP_R2
        1.8%
        54.9%
        51%
        29.1
        NS.1223.004.NEBNext_dual_i7_G1---NEBNext_dual_i5_G1.27_32_vHIPest_lib_complex_metrics
        16.7%
        NS.1223.004.NEBNext_dual_i7_G2---NEBNext_dual_i5_G2.08_09_dHIP
        15.4%
        94.3%
        22.6
        NS.1223.004.NEBNext_dual_i7_G2---NEBNext_dual_i5_G2.08_09_dHIP_R1
        47.4%
        51%
        24.0
        NS.1223.004.NEBNext_dual_i7_G2---NEBNext_dual_i5_G2.08_09_dHIP_R2
        1.8%
        50.7%
        52%
        24.0
        NS.1223.004.NEBNext_dual_i7_G2---NEBNext_dual_i5_G2.08_09_dHIPest_lib_complex_metrics
        14.0%
        NS.1223.004.NEBNext_dual_i7_G3---NEBNext_dual_i5_G3.10_35_ACC
        17.3%
        93.8%
        25.3
        NS.1223.004.NEBNext_dual_i7_G3---NEBNext_dual_i5_G3.10_35_ACC_R1
        48.7%
        50%
        27.0
        NS.1223.004.NEBNext_dual_i7_G3---NEBNext_dual_i5_G3.10_35_ACC_R2
        1.8%
        51.1%
        51%
        27.0
        NS.1223.004.NEBNext_dual_i7_G3---NEBNext_dual_i5_G3.10_35_ACCest_lib_complex_metrics
        15.8%
        NS.1223.004.NEBNext_dual_i7_G4---NEBNext_dual_i5_G4.04_09_vHIP
        18.6%
        94.2%
        30.1
        NS.1223.004.NEBNext_dual_i7_G4---NEBNext_dual_i5_G4.04_09_vHIP_R1
        52.4%
        51%
        31.9
        NS.1223.004.NEBNext_dual_i7_G4---NEBNext_dual_i5_G4.04_09_vHIP_R2
        1.7%
        55.6%
        51%
        31.9
        NS.1223.004.NEBNext_dual_i7_G4---NEBNext_dual_i5_G4.04_09_vHIPest_lib_complex_metrics
        17.0%
        NS.1223.004.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.13_09_dHIP
        19.8%
        94.5%
        36.4
        NS.1223.004.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.13_09_dHIP_R1
        52.5%
        51%
        38.5
        NS.1223.004.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.13_09_dHIP_R2
        1.7%
        55.9%
        51%
        38.5
        NS.1223.004.NEBNext_dual_i7_G5---NEBNext_dual_i5_G5.13_09_dHIPest_lib_complex_metrics
        18.2%
        NS.1223.004.NEBNext_dual_i7_G6---NEBNext_dual_i5_G6.01_15_ACC
        16.5%
        94.0%
        21.8
        NS.1223.004.NEBNext_dual_i7_G6---NEBNext_dual_i5_G6.01_15_ACC_R1
        46.3%
        51%
        23.2
        NS.1223.004.NEBNext_dual_i7_G6---NEBNext_dual_i5_G6.01_15_ACC_R2
        1.8%
        49.1%
        51%
        23.2
        NS.1223.004.NEBNext_dual_i7_G6---NEBNext_dual_i5_G6.01_15_ACCest_lib_complex_metrics
        15.2%
        NS.1223.004.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.25_31_vHIP
        18.7%
        93.9%
        29.5
        NS.1223.004.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.25_31_vHIP_R1
        52.1%
        51%
        31.4
        NS.1223.004.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.25_31_vHIP_R2
        1.7%
        55.4%
        51%
        31.4
        NS.1223.004.NEBNext_dual_i7_G7---NEBNext_dual_i5_G7.25_31_vHIPest_lib_complex_metrics
        17.1%
        NS.1223.004.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.11_09_dHIP
        16.4%
        94.0%
        26.1
        NS.1223.004.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.11_09_dHIP_R1
        49.0%
        50%
        27.7
        NS.1223.004.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.11_09_dHIP_R2
        1.8%
        51.6%
        51%
        27.7
        NS.1223.004.NEBNext_dual_i7_G8---NEBNext_dual_i5_G8.11_09_dHIPest_lib_complex_metrics
        15.0%
        NS.1223.004.NEBNext_dual_i7_G9---NEBNext_dual_i5_G9.03_32_ACC
        18.3%
        93.6%
        25.3
        NS.1223.004.NEBNext_dual_i7_G9---NEBNext_dual_i5_G9.03_32_ACC_R1
        49.4%
        51%
        27.1
        NS.1223.004.NEBNext_dual_i7_G9---NEBNext_dual_i5_G9.03_32_ACC_R2
        1.8%
        52.1%
        51%
        27.1
        NS.1223.004.NEBNext_dual_i7_G9---NEBNext_dual_i5_G9.03_32_ACCest_lib_complex_metrics
        16.8%
        NS.1223.004.NEBNext_dual_i7_H1---NEBNext_dual_i5_H1.17_32_ACC
        20.2%
        94.0%
        43.8
        NS.1223.004.NEBNext_dual_i7_H1---NEBNext_dual_i5_H1.17_32_ACC_R1
        56.1%
        51%
        46.6
        NS.1223.004.NEBNext_dual_i7_H1---NEBNext_dual_i5_H1.17_32_ACC_R2
        1.8%
        59.1%
        51%
        46.6
        NS.1223.004.NEBNext_dual_i7_H1---NEBNext_dual_i5_H1.17_32_ACCest_lib_complex_metrics
        18.3%
        NS.1223.004.NEBNext_dual_i7_H2---NEBNext_dual_i5_H2.08_09_vHIP
        18.7%
        94.0%
        37.1
        NS.1223.004.NEBNext_dual_i7_H2---NEBNext_dual_i5_H2.08_09_vHIP_R1
        53.8%
        50%
        39.5
        NS.1223.004.NEBNext_dual_i7_H2---NEBNext_dual_i5_H2.08_09_vHIP_R2
        1.8%
        56.5%
        51%
        39.5
        NS.1223.004.NEBNext_dual_i7_H2---NEBNext_dual_i5_H2.08_09_vHIPest_lib_complex_metrics
        17.0%
        NS.1223.004.NEBNext_dual_i7_H3---NEBNext_dual_i5_H3.10_35_dHIP
        18.1%
        94.5%
        37.5
        NS.1223.004.NEBNext_dual_i7_H3---NEBNext_dual_i5_H3.10_35_dHIP_R1
        52.9%
        51%
        39.7
        NS.1223.004.NEBNext_dual_i7_H3---NEBNext_dual_i5_H3.10_35_dHIP_R2
        1.8%
        55.4%
        51%
        39.7
        NS.1223.004.NEBNext_dual_i7_H3---NEBNext_dual_i5_H3.10_35_dHIPest_lib_complex_metrics
        16.4%
        NS.1223.004.NEBNext_dual_i7_H4---NEBNext_dual_i5_H4.08_31_ACC
        18.2%
        93.6%
        29.2
        NS.1223.004.NEBNext_dual_i7_H4---NEBNext_dual_i5_H4.08_31_ACC_R1
        51.1%
        51%
        31.2
        NS.1223.004.NEBNext_dual_i7_H4---NEBNext_dual_i5_H4.08_31_ACC_R2
        1.7%
        53.8%
        51%
        31.2
        NS.1223.004.NEBNext_dual_i7_H4---NEBNext_dual_i5_H4.08_31_ACCest_lib_complex_metrics
        16.6%
        NS.1223.004.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.13_09_vHIP
        17.5%
        93.7%
        30.0
        NS.1223.004.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.13_09_vHIP_R1
        50.1%
        51%
        32.0
        NS.1223.004.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.13_09_vHIP_R2
        1.8%
        53.2%
        51%
        32.0
        NS.1223.004.NEBNext_dual_i7_H5---NEBNext_dual_i5_H5.13_09_vHIPest_lib_complex_metrics
        16.0%
        NS.1223.004.NEBNext_dual_i7_H6---NEBNext_dual_i5_H6.01_15_dHIP
        17.2%
        94.1%
        26.3
        NS.1223.004.NEBNext_dual_i7_H6---NEBNext_dual_i5_H6.01_15_dHIP_R1
        48.8%
        51%
        28.0
        NS.1223.004.NEBNext_dual_i7_H6---NEBNext_dual_i5_H6.01_15_dHIP_R2
        2.0%
        50.6%
        51%
        28.0
        NS.1223.004.NEBNext_dual_i7_H6---NEBNext_dual_i5_H6.01_15_dHIPest_lib_complex_metrics
        15.7%
        NS.1223.004.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.05_13_ACC
        19.6%
        93.9%
        32.2
        NS.1223.004.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.05_13_ACC_R1
        53.0%
        51%
        34.3
        NS.1223.004.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.05_13_ACC_R2
        1.9%
        55.3%
        51%
        34.3
        NS.1223.004.NEBNext_dual_i7_H7---NEBNext_dual_i5_H7.05_13_ACCest_lib_complex_metrics
        17.9%
        NS.1223.004.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.11_09_vHIP
        19.2%
        94.0%
        44.8
        NS.1223.004.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.11_09_vHIP_R1
        55.1%
        50%
        47.6
        NS.1223.004.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.11_09_vHIP_R2
        1.9%
        56.9%
        51%
        47.6
        NS.1223.004.NEBNext_dual_i7_H8---NEBNext_dual_i5_H8.11_09_vHIPest_lib_complex_metrics
        17.4%
        NS.1223.004.NEBNext_dual_i7_H9---NEBNext_dual_i5_H9.03_32_dHIP
        17.9%
        94.1%
        33.5
        NS.1223.004.NEBNext_dual_i7_H9---NEBNext_dual_i5_H9.03_32_dHIP_R1
        51.8%
        50%
        35.6
        NS.1223.004.NEBNext_dual_i7_H9---NEBNext_dual_i5_H9.03_32_dHIP_R2
        2.0%
        53.3%
        51%
        35.6
        NS.1223.004.NEBNext_dual_i7_H9---NEBNext_dual_i5_H9.03_32_dHIPest_lib_complex_metrics
        16.3%
        STAR_rrna_results
        0.0%
        0.0

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Mark Duplicates

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Salmon

        Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.

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        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

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        Gene Counts

        Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

           
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        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        144 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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